[English] 日本語
Yorodumi
- PDB-1sol: A PIP2 AND F-ACTIN-BINDING SITE OF GELSOLIN, RESIDUE 150-169 (NMR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sol
TitleA PIP2 AND F-ACTIN-BINDING SITE OF GELSOLIN, RESIDUE 150-169 (NMR, AVERAGED STRUCTURE)
ComponentsGELSOLIN (150-169)
KeywordsACTIN-BINDING PROTEIN
Function / homology
Function and homology information


striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / regulation of podosome assembly / sequestering of actin monomers / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / cardiac muscle cell contraction / cell projection assembly / podosome / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cortical actin cytoskeleton / phagocytosis, engulfment / hepatocyte apoptotic process / sarcoplasm / cilium assembly / Caspase-mediated cleavage of cytoskeletal proteins / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / phagocytic vesicle / actin filament polymerization / central nervous system development / actin filament organization / protein destabilization / cellular response to type II interferon / actin filament binding / actin cytoskeleton / lamellipodium / actin binding / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / blood microparticle / Amyloid fiber formation / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / extracellular space / extracellular exosome / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Villin/Gelsolin / Gelsolin homology domain / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
MethodSOLUTION NMR
AuthorsXian, W. / Vegners, R. / Janmey, P.A. / Braunlin, W.H.
Citation
Journal: Biophys.J. / Year: 1995
Title: Spectroscopic studies of a phosphoinositide-binding peptide from gelsolin: behavior in solutions of mixed solvent and anionic micelles.
Authors: Xian, W. / Vegners, R. / Janmey, P.A. / Braunlin, W.H.
#1: Journal: J.Biol.Chem. / Year: 1992
Title: Phosphoinositide-Binding Peptides Derived from the Sequences of Gelsolin and Villin
Authors: Janmey, P.A. / Lamb, J. / Allen, P.G. / Matsudaira, P.T.
History
DepositionSep 29, 1995Processing site: BNL
Revision 1.0Mar 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GELSOLIN (150-169)


Theoretical massNumber of molelcules
Total (without water)2,3951
Polymers2,3951
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

-
Components

#1: Protein/peptide GELSOLIN (150-169)


Mass: 2394.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source / References: UniProt: P06396

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Crystal grow
*PLUS
Method: other

-
Processing

NMR softwareName: SYBYL / Version: 6 / Developer: TRIPOS ASSOCIATES / Classification: refinement
NMR ensembleConformers submitted total number: 1

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more